DB code: S00237

CATH domain 3.20.20.210 : TIM Barrel Catalytic domain
E.C. 4.1.1.37
CSA 1uro
M-CSA 1uro
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P06132 Uroporphyrinogen decarboxylase
UPD
URO-D
EC 4.1.1.37
NP_000365.3 (Protein)
NM_000374.4 (DNA/RNA sequence)
PF01208 (URO-D)
[Graphical View]

KEGG enzyme name
uroporphyrinogen decarboxylase
uroporphyrinogen III decarboxylase
porphyrinogen carboxy-lyase
porphyrinogen decarboxylase
uroporphyrinogen-III carboxy-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P06132 DCUP_HUMAN Uroporphyrinogen III = coproporphyrinogen + 4 CO(2). Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00860 Porphyrin and chlorophyll metabolism

Compound table
Substrates Products Intermediates
KEGG-id C01051 C00011 C03263
E.C.
Compound Uroporphyrinogen III CO2 Coproporphyrinogen III
Type aromatic ring (with nitrogen atoms),carboxyl group others aromatic ring (with nitrogen atoms),carboxyl group
ChEBI 15437
16526
15439
PubChem 1179
280
321
1uroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1jphA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1jpiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1jpkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature;[8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1uroA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 86
1jphA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 86 mutant I260T
1jpiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 86 mutant F232L
1jpkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 86 mutant G156D

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Scheme 11, p.27-28 4
[5]
Scheme 3, p.134-137 3
[8]
p.2467-2468

References
[1]
Resource
Comments
Medline ID
PubMed ID 3895052
Journal Nat Prod Rep
Year 1985
Volume 2
Pages 19-47
Authors Leeper FJ
Title The biosynthesis of porphyrins, chlorophylls, and vitamin B12.
Related PDB
Related UniProtKB
[2]
Resource
Comments VARIANT PCT GLU-281.
Medline ID 87042763
PubMed ID 3775362
Journal Science
Year 1986
Volume 234
Pages 732-4
Authors de Verneuil H, Grandchamp B, Beaumont C, Picat C, Nordmann Y
Title Uroporphyrinogen decarboxylase structural mutant (Gly281----Glu) in a case of porphyria.
Related PDB
Related UniProtKB P06132
[3]
Resource
Comments
Medline ID
PubMed ID 2180703
Journal Eur J Biochem
Year 1990
Volume 188
Pages 393-403
Authors Felix F, Brouillet N
Title Purification and properties of uroporphyrinogen decarboxylase from Saccharomyces cerevisiae. Yeast uroporphyrinogen decarboxylase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1576986
Journal Eur J Biochem
Year 1992
Volume 205
Pages 1011-6
Authors Garey JR, Labbe-Bois R, Chelstowska A, Rytka J, Harrison L, Kushner J, Labbe P
Title Uroporphyrinogen decarboxylase in Saccharomyces cerevisiae. HEM12 gene sequence and evidence for two conserved glycines essential for enzymatic activity.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7842850
Journal Ciba Found Symp
Year 1994
Volume 180
Pages 131-51; discussion 152-5
Authors Akhtar M
Title The modification of acetate and propionate side chains during the biosynthesis of haem and chlorophylls: mechanistic and stereochemical studies.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9194196
Journal Protein Sci
Year 1997
Volume 6
Pages 1343-6
Authors Phillips JD, Whitby FG, Kushner JP, Hill CP
Title Characterization and crystallization of human uroporphyrinogen decarboxylase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9761933
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 476-8
Authors Laterriere M, d'Estaintot BL, Dautant A, Precigoux G, Hombrados I, De Verneuil H
Title Expression, purification, crystallization and preliminary X-ray diffraction analysis of human uroporphyrinogen decarboxylase.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 98232492
PubMed ID 9564029
Journal EMBO J
Year 1998
Volume 17
Pages 2463-71
Authors Whitby FG, Phillips JD, Kushner JP, Hill CP
Title Crystal structure of human uroporphyrinogen decarboxylase.
Related PDB 1uro
Related UniProtKB P06132
[9]
Resource
Comments
Medline ID
PubMed ID 11719352
Journal Blood
Year 2001
Volume 98
Pages 3179-85
Authors Phillips JD, Parker TL, Schubert HL, Whitby FG, Hill CP, Kushner JP
Title Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase.
Related PDB 1jph 1jpi 1jpk
Related UniProtKB

Comments

Created Updated
2004-03-30 2009-02-26